library(qtl2)
library(evir)
source('/Users/bakerr/Dropbox (UMass Medical School)/clusters2/plot_effects_CC.R')
load("/Users/bakerr/Desktop/TIMBR/reduced_map_qtl2_mapping_objects.Rdata")
map <- map.1 # for use with legacy code

Load phenotype matrix and scan results.

pheno <- read.csv("pheno_eigenscores_from_WGCNA_all60_win.csv", row.names=1)
load("43478_all60_eigenscores_win_scan1_out.Rdata")

Allele effects.

map.Mb <- qtl2convert::map_df_to_list(GM.snps, chr_column="Chrom", pos_column="pos", Xchr="X")
for (i in colnames(pheno)) {
  plot.effects.CC(genoprobs.1, map.Mb, pheno, i, 10, out.cov, i)
}

BLUP’s of effects – SKIPPED

for (i in colnames(pheno)) {
  plot.effects.CC(genoprobs.1, map.Mb, pheno, i, 10, out.cov, i, blup=T)
}